The Construction And Analyses Of Databases For Hypersensitive Response Of Phytopathogens

Hypersensitive Response (HR) is some kind of Resistance Response induced by pathogens when they infect their plant host, studies on which have great significance in the understanding of the mechanisms of pathogen's infection and host's resistance.In the genomes of phytopathogens, Hypersensitive Response and Pathogenicity genes (hrp genes) mainly code for type â…¢ secretion system protein and determine the pathogenicity of pathogens to their plant host.To study HR genes and their products, we constructed the Hypersensitive Response (HR) database serving at http://sdbi.sdut.edu.cn/hrp/index.php for public access. HR database totally contains 3363 HR genes and their protein products, each entry of which includes the information of gene name, species origin, DNA sequence, protein sequence etc. This database also contains the complete genomes of some important phytopathogens. Additionally, for the purpose of easy use, we also provide convenient tools for sequence query and comparison, including the famous alignment program-BLAST.Four phytopathogens' genomes are analyzed using approaches of Z' curve, Codon Usage Bias and Amino Acid Usage Bias. Result shows that genes of hrp Pathogenicity Island (PAI) are apparently different from the genome in GC-content and their protein products have different Codon Usage and Amino Acid Preference from other genes of the same genome. This difference manifested in some degree the hypothesis that most HR genes are Horizontally Transferred Genes.In bacteria genomes, genes coding for ribosome protein, transcription factor protein and molecular chaperone protein are acknowledged as 3 representatives of highly expressed genes. Hereby, we selected 5 phytopathogens, and using Karllin's approach of calculating the difference between a gene and a gene group, we calculated the codon usage preference and amino acid usage preference of HR genes compared with the 3 kinds of highly expressed genes and the total genes of the whole genome. Results suggest that HR genes are more like ordinary genomic genes ratherthan predicted highly expressed genes in the characteristics of sequence composition, which consists with the experiment result that HR genes do not code for essential proteins and their loss does not affect pathogens' living on a basic culture medium. In the results, we also found that genes coding for flagellar protein -HR proteins' homological protein- have higher predicted expression level. Moreover, we also investigated the top 20 predicted highly expressed genes from 5 pathogens' genomes, and found that except for the 3 kinds of representative highly expressed genes, genes coding for metabolic pathway proteins, pathogenicity related proteins, ATP synthase subunits and many Transporters & Channels proteins are also predicted highly expressed.Based on the above analysis, we provide some new clues on the probability of PrhA protein, Flagellin protein fliC, Type III secretion system, etc as targets of novel designed pesticides.